Oligonucleotides are known to hybridize to single-stranded DNA or RNA molecules. Hybridization is the sequence-specific base pair hydrogen bonding of nucleobases of the oligonucleotides to nucleobases of target DNA or RNA. Such nucleobase pairs are said to be complementary to one another.
The complementarity of oligonucleotides has been used for inhibition of a number of cellular targets. Such complementary oligonucleotides are commonly described as being antisense oligonucleotides. Various reviews describing the results of these studies have been published including Progress In Antisense Oligonucleotide Therapeutics, Crooke, S. T. and Bennett, C. F., Annu. Rev. Pharmacol. Toxicol., 1996, 36, 107-129. These oligonucleotides have proven to be very powerful research tools and diagnostic agents. Further, certain oligonucleotides that have been shown to be efficacious are currently in human clinical trials. Antisense therapy involves the use of oligonucleotides having complementary sequences to target RNA or DNA. The antisense oligonucleotide binds to the target RNA or DNA. Upon binding to the target RNA or DNA, the antisense oligonucleotide can selectively inhibit the genetic expression of these nucleic acids or can induce some other events such as destruction of a targeted RNA or DNA or activation of gene expression.
Destruction of targeted RNA can be effected by RNase H activation. RNase H is an endonuclease that cleaves the RNA strand of DNA:RNA duplexes. This enzyme, thought to play a role in DNA replication, has been shown to be capable of cleaving the RNA component of the DNA:RNA duplexes in cell free systems as well as in Xenopus oocytes.
RNase H is very sensitive to structural alterations in antisense oligonucleotides. To activate RNase H, a DNA:RNA structure must be formed. Therefore for an antisense oligonucleotide to activate RNase H, at least a part of the oligonucleotide must be DNA like. To be DNA like requires that the sugars of the nucleotides of the oligonucleotide have a 2'-deoxy structure and the phosphate linkages of the oligonucleotide have negative charges. Chemical modifications of the DNA portion of oligonucleotide at either of these two positions resulted in oligonucleotides that are no longer substrates for RNase H.
However, 2'-deoxy nucleotides have weaker binding affinity to their counterpart ribonucleotides than like ribonucleotides would, i.e., RNA:RNA binding is stronger than DNA:RNA binding, and the presence of the negative charges has been though to contribute to reduced cellular uptake of the antisense oligonucleotide. Therefore, to circumvent the limitations of DNA like oligonucleotides, chimeric oligonucleotides have been synthesized wherein a DNA like central portion having 2'-deoxy nucleotides and negative charged phosphate linkages is included as the center of a large oligonucleotide that has other types of nucleotides on either side of the DNA like center portion. The center portion must be of a certain size in order to activate RNase H upon binding of the oligonucleotide to a target RNA.
Accordingly, there remains a continuing long-felt need for modified antisense compounds that incorporate chemical modifications for improving characteristics such as compound stability and cellular uptake but are also available for regulation of target RNA through each of the known mechanism of action of antisense compounds including RNase H. Such regulation of target RNA would be useful for therapeutic purposes both in vivo and ex vivo and, as well as, for diagnostic reagents and as research reagents including reagents for the study of both cellular and in vitro events.